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Surveying of Acid-Tolerant Thermophilic Lignocellulolytic Fungi in Vietnam

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Surveying of Acid-Tolerant Thermophilic Lignocellulolytic Fungi in Vietnam www.nature.com/scientificreports OPEN Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high Received: 2 October 2018 Accepted: 23 January 2019 genetic diversity Published: xx xx xxxx Vu Nguyen Thanh 1, Nguyen Thanh Thuy1, Han Thi Thu Huong1, Dinh Duc Hien1, Dinh Thi My Hang1, Dang Thi Kim Anh1, Silvia Hüttner 2, Johan Larsbrink 2 & Lisbeth Olsson2 Thermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genus Thielavia, but they represented 23 highly divergent genetic groups diferent from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at diferent pH and temperatures. The endoglucanase and xylanase activities difered substantially between the diferent species and strains, but in general, the enzymes produced by the novel Thielavia spp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics. Termotolerance is not very common among eukaryotes. While the upper temperature limit for the growth of prokaryotes has been reported to be 121 °C1, the highest growth temperature of eukaryotes is around 60–62 °C2, and only a small number of fungal species thrive at such high temperatures. Among the estimated 3.0 million fungal species existing in nature, and approximately 100 000 species described, only about 50 species have been found to be able to grow at 50–60 °C3. Tese species are limited to the Sordariales, Eurotiales, and Onygenales in the Ascomycota and the Mucorales of the Zygomycota. No representative of thermophilic Basidiomycota has yet been confrmed4. Fungi capable of growing at elevated temperatures are classifed into thermophilic and thermo- tolerant groups. Tere is no consensus on the demarcation between the two groups, but typically, a fungus that has a thermal maximum near 50 °C and a minimum below 20 °C is regarded as thermotolerant, while those that grow at 50 °C or above, but not grow at 20 °C or above5 are regarded as thermophilic. In the present study, the cultivation temperature was maintained at 50 °C during initial screening for thermophilic fungi. Earlier reports of thermophilic fungi were the result of accidental contamination of organic materials incu- bated at elevated temperatures. Tese include the isolation of Mucor pusillus (=Rhizomucor pusillus) from bread in 1886, and Humicola lanuginosa (=Termomyces lanuginosus) from potato slices in 1899 (from Johri et al.6). It was later found that thermophilic fungi are a regular microbial component of self-heating decomposing hay7. In natural environments, thermophilic fungi are most commonly found in rapidly decomposing plant residues, where heat is generated through exothermic microbial activity. Heat accumulation in a 5-cm layer of leaf litter is sufcient to create favourable conditions for thermophilic fungi, and temperature increase may even lead to igni- tion in stockpiles of hay, oil seeds or manure. Most thermophilic fungi also grow well at moderate temperatures 1Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam. 2Wallenberg Wood Science Center, Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. Correspondence and requests for materials should be addressed to V.N.T. (email: [email protected]) SCIENTIFIC REPORTS | (2019) 9:3674 | https://doi.org/10.1038/s41598-019-40213-5 1 www.nature.com/scientificreports/ www.nature.com/scientificreports and can be found in various substrates, including soils, composts, piles of hay, stored grains, wood chip piles, nesting materials of birds and animals or in municipal refuse8. While thermotolerant/thermophilic fungi appear to be exceedingly rare, fungi able to tolerate acidic condi- tions are frequently encountered in nature, and many species have been shown to be capable of growing at pH lev- els as low as 29. Tere is no clear demarcation between acidophilic and acid-tolerant fungi, but it is ofen assumed that acidophilic fungi are those that can grow at pH 1.0 and have optimum growth at pH 3.0 or below10. Hereafer, we refer to acidophilic species as those optimally growing at pH values below 3, while acidotolerant species refer to species able to grow in acidic environments but with growth optima above pH 3. Te earliest description of aci- dophilic fungi dates back to 1943, when a strain of Acontium velatum and a “Fungus D” were shown to be capable of growing in glucose medium containing 1.25 M sulphuric acid at pH 011. Unfortunately, the strain of Acontium velatum appears to have been lost since the initial publication, but “Fungus D” is now believed to be a strain of Acidomyces acidophilus which is commonly found in extremely acidic environments12. Until now, acidophility has been shown for only 6 fungal species, including Acidomyces acidophilus (MB#511856) (=Scytalidium acido- philum = Acidomyces richmondensis = Fungus D), Acidomyces acidothermus (MB#564520), Acidothrix acidophila (MB#805424), Acidea extrema (MB#805425), Acontium velatum (MB#142596, no living specimen available) and Hortaea acidophila (MB#367373) (=Neohortaea acidophila). Te strain Bispora sp. MEY-1, well-known for the production of a range of thermophilic and acid-tolerant lignocellulolytic enzymes13, probably belongs to the spe- cies Acidomyces acidothermus14. Phylogenetically, all acidophilic species are Ascomycota, and the teleomorphic state is known only for Acidomyces acidothermus (described as Teratosphaeria acidotherma, MB#517415)14. Termophilic and acid-tolerant fungi have received considerable attention, as their thermostable enzymes can be employed in industrial processes at elevated temperatures. Increasing the process temperature can have advantages, for example, increasing the rate of chemical reactions, decreasing the viscosity of substrates and reducing the risk of contamination by mesophilic microorganisms15. A number of enzymes such as amylases, cellulases, xylanases, lipases and proteases from thermophilic fungi have been found to be thermostable6. Te lipase and rennet from Rhizomucor miehei are commercial enzymes that fnd wide applications in the food indus- try16. A range of genes encoding lignocellulolytic enzymes in the acidophilic fungus Acidomyces acidothermus MEY-1 has been cloned and expressed. Te enzymes were found to be thermotolerant and functional under acidic conditions13. As a result of increased interest in renewable sources of energy and biomaterials, fungi that are adapted to extreme environmental conditions have recently received special interest as sources of novel hydrolytic enzymes suitable for various technological applications. Genome sequences have been obtained for a large number of thermophilic fungi, such as Myceliophthora thermophila, Tielavia terrestris, Tielavia heterothallica, Chaetomium thermophilum, Termomyces lanuginosus, T. thermophilus, Rhizomucor miehei, Talaromyces cellulolyticus and Malbranchea cinnamomea, as well as for acidophilic fungi, including Acidothrix acidophila, Acidomyces acidophi- lus and Hortaea acidophila17. Genomes of thermophilic lignocellulose-degrading fungi such as Termothelomyces thermophila18, Tielavia terrestris18, and Malbranchea cinnamomea19 have been found to harbour large numbers of carbohydrate-active enzymes (CAZymes). For examples, Tielavia terrestris genome encodes 473 CAZymes, including 212 glycoside hydrolases (GHs), 91 glycosyl transferases (GTs), 4 polysaccharide lyases (PLs), 28 carbohydrate esterases (CEs), 58 enzymes with auxiliary activities (AAs) and 80 carbohydrate-binding modules (CBMs). Compared to the well-known cellulase-producer Trichoderma reesei, Tielavia terrestris has a similar setup of GHs18. Trough stud- ies of the genomes of thermophilic fungi compared to related mesophiles, it appears that common strategies for thermal adaptation include a reduction of the genome size and an increased frequency of the amino acids Ile, Val, Tyr, Trp, Arg, Glu, and Leu (IVYWREL) in proteins20. Although high GC mol% is ofen assumed to contribute to the genome stability at elevated temperatures, the correlation between GC content and thermophilicity in fungi remains inconclusive21. To take advantage of the high fungal biodiversity in the tropics, we have conducted a search in Vietnam for novel fungi for the production of lignocellulolytic enzymes applicable in agriculture and the bioconversion of plant biomass. In a previous study, we reported on the screening of 1100 mesophilic fungal isolates from decaying plant tissue for cellulase, xylanase and accessory enzyme activities22. In the present work, we aimed to explore the biodiversity in northern Vietnam to identify flamentous fungi able to grow at elevated temperatures (50 °C) under extremely
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